Understanding pseudo-albinism in sole (Solea senegalensis): a transcriptomics and metagenomics approach

Pseudo-albinism is a pigmentation disorder observed in flatfish aquaculture with a complex, multi-factor aetiology. We tested the hypothesis that pigmentation abnormalities are an overt signal of more generalised modifications in tissue structure and function, using as a model the Senegalese sole and two important innate immune barriers, the skin and intestine, and their microbiomes. Stereological analyses in pseudo-albino sole revealed a significantly increased mucous cell number in skin (P < 0.001) and a significantly thicker muscle layer and lamina propria in gut (P < 0.001). RNA-seq transcriptome analysis of the skin and gut identified 573 differentially expressed transcripts (DETs, FDR < 0.05) between pseudo-albino and pigmented soles (one pool/tissue from 4 individuals/phenotype). DETs were mainly linked to pigment production, skin structure and regeneration and smooth muscle contraction. The microbiome (16 S rRNA analysis) was highly diverse in pigmented and pseudo-albino skin but in gut had low complexity and diverged between the two pigmentation phenotypes. Quantitative PCR revealed significantly lower loads of Mycoplasma (P < 0.05) and Vibrio bacteria (P < 0.01) in pseudo-albino compared to the control. The study revealed that pseudo-albinism in addition to pigmentation changes was associated with generalised changes in the skin and gut structure and a modification in the gut microbiome.Agência financiadora H2020 European Funds MSCA-RISE project 691102 Portuguese national funds from FCT - Foundation for Science and Technology UID/Multi/04326/2019 Portuguese national funds from the operational programme CRESC Algarve 2020 EMBRC. PT ALG-01-0145-FEDER-022121 Portuguese national funds from the operational programme COMPETE 2020 EMBRC. PT ALG-01-0145-FEDER-022121 European Union (EU) 654008 Fundacao para a Ciencia e a Tecnologia (FCT) SFRH/BPD/84033/2012 Portuguese Institute for Employment and Vocational Training 0068/ET/18info:eu-repo/semantics/publishedVersio

Influence of the ovine genital tract microbiota on the species artificial insemination outcome. A pilot study in commercial sheep farms

To date, there is a lack of research into the vaginal and sperm microbiome and its bearing on artificial insemination (AI) success in the ovine species. Using hypervariable regions V3–V4 of the 16S rRNA, we describe, for the first time, the combined effect of the ovine microbiome of both females (50 ewes belonging to five herds) and males (five AI rams from an AI center) on AI outcome. Differences in microbiota abundance between pregnant and non-pregnant ewes and between ewes carrying progesterone-releasing intravaginal devices (PRID) with or without antibiotic were tested at different taxonomic levels. The antibiotic treatment applied with the PRID only altered Streptobacillus genus abundance, which was significantly lower in ewes carrying PRID with antibiotic. Mageebacillus, Histophilus, Actinobacilllus and Sneathia genera were significantly less abundant in pregnant ewes. In addition, these genera were more abundant in two farms with higher AI failure. Species of these genera such as Actinobacillus seminis and Histophilus somni have been associated with reproductive disorders in the ovine species. These genera were not present in the sperm samples of AI rams, but were found in the foreskin samples of rams belonging to herd 2 (with high AI failure rate) indicating that their presence in ewes’ vagina could be due to prior transmission by natural mating with rams reared in the herd

CO19 168. Impacto de la hipertensión pulmonar en la evolución de los ancianos sometidos a sustitución valvular aórtica

ObjetivoEstudiar la influencia de la hipertensión pulmonar (HTP) en la evolución de los ancianos sometidos a sustitución valvular aórtica (SVA).Material y métodosDesde octubre de 1999 hasta noviembre de 2009, 517 ancianos (rango 70-87 años) fueron sometidos a SVA. Trescientos cincuenta y cinco (68,7%) enfermos (grupo I) tenían hipertensión pulmonar (ligera 157; moderada 149; grave 49) frente a 162 (31,3%) (grupo II) con presiones pulmonares normales. El seguimiento medio fue de 4,3 años.ResultadosLa edad media fue de 76,4±3,9 años. La fibrilación auricular (29,5 vs 5,6%; p=0,001) y la insuficiencia mitral moderada preoperatorias (13,7 vs 5,1%; p=0,003) fueron más frecuentes en el grupo I. La mortalidad hospitalaria fue 4,3%, siendo significativamente superior en los pacientes con HTP (I: 5,7% vs II: 0,8%; p=0,027). Los pacientes con HTP moderada (7,3%) o grave (13,9%) tuvieron una mortalidad significativamente superior a la de los pacientes con HTP ligera (1,7%) (p=0,016). La supervivencia actuarial a los 5 años, de los pacientes dados de alta, aunque superior en los pacientes sin HTP (I: 80,9% vs II: 90,6%; p=0,162), no alcanzó significación. La HTP moderada-grave se asoció de manera independiente a la mortalidad hospitalaria (odds ratio [OR]: 2,07; p=0,015), pero no a una menor supervivencia en el seguimiento.ConclusionesLa HTP moderada-grave es un factor de riesgo independiente de mortalidad hospitalaria en los ancianos sometidos a SVA. Su influencia en la supervivencia a medio plazo es menos clara

Computing and visually analyzing mutual information in molecular co-evolution

<p>Abstract</p> <p>Background</p> <p>Selective pressure in molecular evolution leads to uneven distributions of amino acids and nucleotides. In fact one observes correlations among such constituents due to a large number of biophysical mechanisms (folding properties, electrostatics, ...). To quantify these correlations the mutual information -after proper normalization - has proven most effective. The challenge is to navigate the large amount of data, which in a study for a typical protein cannot simply be plotted.</p> <p>Results</p> <p>To visually analyze mutual information we developed a matrix visualization tool that allows different views on the mutual information matrix: filtering, sorting, and weighting are among them. The user can interactively navigate a huge matrix in real-time and search e.g., for patterns and unusual high or low values. A computation of the mutual information matrix for a sequence alignment in FASTA-format is possible. The respective stand-alone program computes in addition proper normalizations for a null model of neutral evolution and maps the mutual information to <it>Z</it>-scores with respect to the null model.</p> <p>Conclusions</p> <p>The new tool allows to compute and visually analyze sequence data for possible co-evolutionary signals. The tool has already been successfully employed in evolutionary studies on HIV1 protease and acetylcholinesterase. The functionality of the tool was defined by users using the tool in real-world research. The software can also be used for visual analysis of other matrix-like data, such as information obtained by DNA microarray experiments. The package is platform-independently implemented in <monospace>Java</monospace> and free for academic use under a GPL license.</p

The Fittest versus the Flattest: Experimental Confirmation of the Quasispecies Effect with Subviral Pathogens

The “survival of the fittest” is the paradigm of Darwinian evolution in which the best-adapted replicators are favored by natural selection. However, at high mutation rates, the fittest organisms are not necessarily the fastest replicators but rather are those that show the greatest robustness against deleterious mutational effects, even at the cost of a low replication rate. This scenario, dubbed the “survival of the flattest”, has so far only been shown to operate in digital organisms. We show that “survival of the flattest” can also occur in biological entities by analyzing the outcome of competition between two viroid species coinfecting the same plant. Under optimal growth conditions, a viroid species characterized by fast population growth and genetic homogeneity outcompeted a viroid species with slow population growth and a high degree of variation. In contrast, the slow-growth species was able to outcompete the fast species when the mutation rate was increased. These experimental results were supported by an in silico model of competing viroid quasispecies

La investigación en Pediatría en España: retos y prioridades. Plataforma INVEST-AEP

La investigación clínica es la piedra angular para el desarrollo de la Medicina, y, en el ámbito de la Pediatría, supone un reto adicional debido a las peculiaridades que diferencian a los niños de los adultos. A pesar del enorme impacto de la salud infantil en el resto de la vida, nuestra sociedad aún no está suficientemente concienciada sobre la importancia de la investigación pediátrica, que, en general, se encuentra también muy alejada del día a día de quienes nos dedicamos a esta profesión. Desde la Asociación Española de Pediatría (AEP) se ha creado una plataforma específica de investigación —INVEST-AEP— para dar respuesta específica a los retos de la investigación en el seno de nuestra sociedad. En este artículo se retrata el escenario actual de la investigación pediátrica en España y se objetivan las metas alcanzadas en los últimos años, gracias al esfuerzo de los pediatras investigadores. Además, se realiza un análisis en profundidad sobre las barreras cotidianas que dificultan el desarrollo amplio y competitivo de la investigación pediátrica, como la falta de incentivación y ausencia de formación específica de pre y posgrado, la elevada carga asistencial o la falta de infraestructuras y financiación específicas. Definimos la misión, visión y valores de INVEST-AEP para tratar de diseñar una «hoja de ruta» para la investigación pediátrica española de los próximos años. Research is the cornerstone of medical progress. Paediatric research has its own nuances and represents an additional challenge due to the intrinsic characteristics of the paediatric population compared with adults. Despite the tremendous importance of childhood health and its impact during adulthood, society is still not convinced about the importance of conducting research in paediatrics. This also applies to paediatricians themselves, who think about research as a discipline that does not directly involve them. The Spanish Academy of Paediatrics has developed a specific research platform- INVEST-AEP- to try to help and answer the challenges associated with paediatric research in the society This article reflects the current status of paediatric research in Spain, and the goals achieved over the last few years due to the effort of paediatric researchers. In addition, a deeper analysis is provided as regards: a) the barriers that represent a hurdle for the development of broad and competitive paediatric research in our day to day work; b) the limited incentives and specific pre- and post-doctoral training; c) the high clinical burden for paediatricians or; d) the lack of specific infrastructure and dedicated funding for paediatrics. The mission, vision and values of INVEST-AEP are to develop an accessible roadmap for the development and implementation of paediatric research in Spain for the next few years

Dynamics of Molecular Evolution and Phylogeography of Barley yellow dwarf virus-PAV

Barley yellow dwarf virus (BYDV) species PAV occurs frequently in irrigated wheat fields worldwide and can be efficiently transmitted by aphids. Isolates of BYDV-PAV from different countries show great divergence both in genomic sequences and pathogenicity. Despite its economical importance, the genetic structure of natural BYDV-PAV populations, as well as of the mechanisms maintaining its high diversity, remain poorly explored. In this study, we investigate the dynamics of BYDV-PAV genome evolution utilizing time-structured data sets of complete genomic sequences from 58 isolates from different hosts obtained worldwide. First, we observed that BYDV-PAV exhibits a high frequency of homologous recombination. Second, our analysis revealed that BYDV-PAV genome evolves under purifying selection and at a substitution rate similar to other RNA viruses (3.158×10−4 nucleotide substitutions/site/year). Phylogeography analyses show that the diversification of BYDV-PAV can be explained by local geographic adaptation as well as by host-driven adaptation. These results increase our understanding of the diversity, molecular evolutionary characteristics and epidemiological properties of an economically important plant RNA virus

Temporal Dynamics of Intrahost Molecular Evolution for a Plant RNA Virus

[EN] Populations of plant RNA viruses are highly polymorphic in infected plants, which may allow rapid within-host evolution. To understand tobacco etch potyvirus (TEV) evolution, longitudinal samples from experimentally evolved populations in the natural host tobacco and from the alternative host pepper were phenotypically characterized and genetically analyzed. Temporal and compartmental variabilities of TEV populations were quantified using high throughput Illumina sequencing and population genetic approaches. Of the two viral phenotypic traits measured, virulence increased in the novel host but decreased in the original one, and viral load decreased in both hosts, though to a lesser extent in the novel one. Dynamics of population genetic diversity were also markedly different among hosts. Population heterozygosity increased in the ancestral host, with a dominance of synonymous mutations fixed, whereas it did not change or even decreased in the new host, with an excess of nonsynonymous mutations. All together, these observations suggest that directional selection is the dominant evolutionary force in TEV populations evolving in a novel host whereas either diversifying selection or random genetic drift may play a fundamental role in the natural host. To better understand these evolutionary dynamics, we developed a computer simulation model that incorporates the effects of mutation, selection, and drift. Upon parameterization with empirical data from previous studies, model predictions matched the observed patterns, thus reinforcing our idea that the empirical patterns of mutation accumulation represent adaptive evolution.The authors thank Francisca de la Iglesia and Paula Agudo for excellent technical assistance, our labmates for useful discussions and suggestions, and Dr Jose A. Daros for gifting us the pMTEV infectious clone. This work was supported by grants BFU2009-06993 and BFU2012-30805 from the Spanish Ministry of Economy and Competitiveness (MINECO), grant PROMETEOII/2014/021 from Generalitat Valenciana, and by the European Commission 7th Framework Programme (FP7-ICT-611640 FET Proactive: Evolving Living Technologies) EvoEvo project to S.F.E. J.M.C. was supported by a JAE-doc postdoctoral contract from CSIC. A.W. was supported by the EvoEvo project. J.H. was recipient of a predoctoral contract from MINECO. M.P.Z. was supported by a Juan de la Cierva postdoctoral contract from MINECO.Cuevas, JM.; Willemsen, A.; Hillung, J.; Zwart, MP.; Elena Fito, SF. (2015). Temporal Dynamics of Intrahost Molecular Evolution for a Plant RNA Virus. Molecular Biology and Evolution. 32(5):1132-1147. https://doi.org/10.1093/molbev/msv028S1132114732

Integrated Analysis of Residue Coevolution and Protein Structure in ABC Transporters

Intraprotein side chain contacts can couple the evolutionary process of amino acid substitution at one position to that at another. This coupling, known as residue coevolution, may vary in strength. Conserved contacts thus not only define 3-dimensional protein structure, but also indicate which residue-residue interactions are crucial to a protein’s function. Therefore, prediction of strongly coevolving residue-pairs helps clarify molecular mechanisms underlying function. Previously, various coevolution detectors have been employed separately to predict these pairs purely from multiple sequence alignments, while disregarding available structural information. This study introduces an integrative framework that improves the accuracy of such predictions, relative to previous approaches, by combining multiple coevolution detectors and incorporating structural contact information. This framework is applied to the ABC-B and ABC-C transporter families, which include the drug exporter P-glycoprotein involved in multidrug resistance of cancer cells, as well as the CFTR chloride channel linked to cystic fibrosis disease. The predicted coevolving pairs are further analyzed based on conformational changes inferred from outward- and inward-facing transporter structures. The analysis suggests that some pairs coevolved to directly regulate conformational changes of the alternating-access transport mechanism, while others to stabilize rigid-body-like components of the protein structure. Moreover, some identified pairs correspond to residues previously implicated in cystic fibrosis

Phylogenetic Dependency Networks: Inferring Patterns of CTL Escape and Codon Covariation in HIV-1 Gag

HIV avoids elimination by cytotoxic T-lymphocytes (CTLs) through the evolution of escape mutations. Although there is mounting evidence that these escape pathways are broadly consistent among individuals with similar human leukocyte antigen (HLA) class I alleles, previous population-based studies have been limited by the inability to simultaneously account for HIV codon covariation, linkage disequilibrium among HLA alleles, and the confounding effects of HIV phylogeny when attempting to identify HLA-associated viral evolution. We have developed a statistical model of evolution, called a phylogenetic dependency network, that accounts for these three sources of confounding and identifies the primary sources of selection pressure acting on each HIV codon. Using synthetic data, we demonstrate the utility of this approach for identifying sites of HLA-mediated selection pressure and codon evolution as well as the deleterious effects of failing to account for all three sources of confounding. We then apply our approach to a large, clinically-derived dataset of Gag p17 and p24 sequences from a multicenter cohort of 1144 HIV-infected individuals from British Columbia, Canada (predominantly HIV-1 clade B) and Durban, South Africa (predominantly HIV-1 clade C). The resulting phylogenetic dependency network is dense, containing 149 associations between HLA alleles and HIV codons and 1386 associations among HIV codons. These associations include the complete reconstruction of several recently defined escape and compensatory mutation pathways and agree with emerging data on patterns of epitope targeting. The phylogenetic dependency network adds to the growing body of literature suggesting that sites of escape, order of escape, and compensatory mutations are largely consistent even across different clades, although we also identify several differences between clades. As recent case studies have demonstrated, understanding both the complexity and the consistency of immune escape has important implications for CTL-based vaccine design. Phylogenetic dependency networks represent a major step toward systematically expanding our understanding of CTL escape to diverse populations and whole viral genes